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Force Field Development

A major obstacle in molecular structure prediction is an insufficient accuracy of the force field. We explored several ideas to improve the accuracy and efficiency, as well as develop terms beneficial for the internal coordinate mechanics.

ICMFF internal coordinate force field

Maxim Totrov's group at Molsoft developed a better peptide forcefield where the originally fixed geometry representation for aminoacids was replaced by models with flexible backbone Ca planar angle. Several other ideas improving the accuracy of the model and the energies have been introduced. See this publication.

Arnautova YA, Abagyan RA, Totrov M
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.
Proteins, 2011 Feb, 79, 477-98, 21069716 , pdf

Parameters can be derived directly from quantum mechanical energies without combination rules

In [Bordner 2003] we demonstrated two that van der Waals energy calculation can be improved if the force field parameters are free from un-physical combination rules. Furthermore, we demonstrated that accurate van der Waals parameters can be derived directly from the calculated quantum mechanical energies (MP2/d-aug-cc-pVDZ level with a counterpoise correction). The derived parameters reproduced experimental values from a validation data set, and this fit was significantly better than the MMFF94 force field. This result can provide a platform for derivation of a new general purpose force field since the benchmark for the force field is no longer limited by scope or accuracy to the experimentally characterized molecules or experimental measurements.

Implicit flexibility model allows to use rigid geometry model with realisti (relaxed) c energy barriers

The ICFF paper explored the implicit flexibility idea into for a fixed covalent geometry force field. See [Katrich, 2004]

Last updated: 2013/05/31